Too much shit going on at once. I have my main quest, I have the riddler "?"s to find. I have the payphones to answer, I have the bane sidequest, I have the random hostages, I have the AR missions, etc...it all litters the map, and instead of feeling like GTA (where you have 2-3 options at a time, mission wise), it feels like I'm being pulled in too many directions at once. This, combined with the crowded controller, and the fact that the city kinda all looks the same (you don't see the variety of zones like you did in the first one), and I think I liked Arkham Asylum better.

edit: Also, the awkward "switch to a different character/part of the story" seems tacked on and unneeded.